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Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil.

The process of composting has been proposed as a biological alternative to improve the quality of tannery sludge (TS) by the action of microbial communities. However, there is limited knowledge about the dynamic of these microbial communities during the composting process. This study assessed the responses of bacterial and archaeal communities during TS composting using the 16S rRNA sequencing. The composting process occurred within 90 days, and samples of compost were collected on day 7 (d7; mesophilic stage), 30 (d30; thermophilic stage), 60 (d60; cooling stage), and 90 (d90; maturation stage). The results showed a succession of microbial phyla during the composting with enrichment of Synergistetes, WS1, and Euryarchaeota at the mesophilic stage, while at the thermophilic stage, there was an enrichment of Hydrogenedentes, WPS-2, Chloroflexi, and Deinococcus-Thermus. At the cooling stage, there was an enrichment of Kiritimatiellaeota, and at the maturation stage, there was an enrichment of Entotheonellaeota, Dadabacteria, Nitrospirae, Dependiatiae, and Fibrobacteres. When analyzing the drivers influencing microbial communities, Cr and pH presented more negative correlations with general phyla. In contrast, S, C, K, temperature, and N presented more positive correlations, while Ni, Cd, and P showed fewer correlations. According to niche occupancy, we observed a decreased proportion of generalists with a consequently increased proportion of specialists following the composting process. This study showed that different stages of the composting present a specific microbial community structure and dynamics, which are related to some specific composting characteristics.

Mixed tree plantations containing nitrogen (N 2 )-fixing species have the potential to enhance C sequestration, soil biodiversity and forest productivity. Here, we investigated the impact of Acacia mangium and Eucalyptus urophilla x E . grandis mixed plantations in the Congolese coastal plains on soil mycobiota community structure and diversity by ITS metabarcoding sequencing and bioinformatic analysis. Higher Faith’s phylogenetic diversity and Evenness’ was found in Eucalyptus monoculture relative to stands containing Acacia. Differences in beta diversity were found among Eucalyptus and Acacia monoculture, and mixed-species stands highlight the effects of plant species on fungal community structure. Ascomycota, Basidiomycota and Rozellomycota phyla were predominant in all stands, with both Dikarya (Ascomycota and Basidiomycota) accounting for more than 70% in all stands. Correlation analysis revealed that sulfur (S) was the most correlated soil attribute with the three predominant phyla but also with Mucoromycota and Calcarisporiellomycota phyla, although mostly negatively correlated (4 out of 5). Phosphorus was mostly positively correlated to soil attributes (3 out of 4) and nitrogen was correlated twice, positively and negatively. Distance-based redundancy analysis revealed a positive correlation of nitrogen (p-value = 0.0019, contribution = 22%) and phosphorus (p-value = 0.0017, contribution = 19%) with soil mycobiota. A high prevalence of generalists (28% to 38%) than specialists (9% to 24%) were found among the different sites. In stands containing Acacia (pure and mixed species) the soil mycobiota harbor the prevalence of generalist strategies with the potential to withstand environmental stresses and utilize a higher number of resources against specialists in Eucalyptus stands. Stronger positive correlation between soil attributes and main fungal taxa, higher generalists’ strategies and lower Faith’s phylogenetic diversity and Evenness were reported in stands containing Acacia. This highlights the potential of mixed-species in preserving community stability following environmental disturbances and increasing the number of resources confirming their important ecological role in boosting the resilience of the forest ecosystems to climate and land-use (plant species as shown by PCA analysis) changes.

Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.

Productivity and sustainability of tropical forest plantations greatly rely on regulation of ecosystem functioning and nutrient cycling, i.e., the link between plant growth, nutrient availability, and the microbial community structure. So far, these interactions have never been evaluated in the Acacia and Eucalyptus forest planted on infertile soils in the Congolese coastal plains. In the present work, the soil bacterial community has been investigated by metabarcoding of the 16S rRNA bacterial gene in different stands of monoculture and mixed-species plantation to evaluate the potential of nitrogen-fixing trees on nutrient and bacterial structure. At the phylum level, the soil bacterial community was dominated by Actinobacteria, followed by Proteobacteria, Firmicutes, and Acidobacteria. A principal coordinate analysis revealed that bacterial communities from pure Eucalyptus, compared to those from plantations containing Acacia in pure and mixed-species stands, showed different community composition (beta-diversity). Regardless of the large variability of the studied soils, the prevalence of Firmicutes phylum, and lower bacterial richness and phylogenic diversity were reported in stands containing Acacia relative to the pure Eucalyptus. Distance-based redundancy analysis revealed a positive correlation of available phosphorus (P) and carbon/nitrogen (C/N) ratio with bacterial community structure. However, the Spearman correlation test revealed a broad correlation between the relative abundance of bacterial taxa and soil attributes, in particular with sulfur (S) and carbon (C), suggesting the important role of soil bacterial community in nutrient cycling in this type of forest management. Concerning mixed plantations, a shift in bacterial community structure was observed, probably linked to other changes, i.e., improvement in soil fertility (enhanced P and C dynamics in forest floor and soil, and increase in soil N status), and C sequestration in both soil and stand wood biomass with the great potential impact to mitigate climate change. Overall, our findings highlight the role of soil attributes, especially C, S, available P, and C/N ratio at a lesser extent, in driving the soil bacterial community in mixed-species plantations and its potential to improve soil fertility and to sustain Eucalyptus plantations established on the infertile and sandy soils of the Congolese coastal plains.

Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.

Seaweed extracts (SEs) and silicon (Si) are known to enhance plant growth under adverse conditions. However, their combined effects on arbuscular mycorrhizal fungi (AMF) are not yet fully understood. This study evaluated the effect of the co-application of an SE and Si on the AMF spore abundance, mycorrhizal colonization, and early growth of Mimosa caesalpiniaefolia. Plants were grown in a greenhouse for 70 days in soil with or without an SE (Solieria filiformis) and three Si levels (0, 150, and 300 mg kg−1). Growth parameters, AMF spore abundance, mycorrhizal colonization, and plant/soil chemical composition were assessed. SE and Si increased the plant height, stem diameter, number of leaves, and shoot dry mass, while higher Si levels reduced the root dry mass and length. Mycorrhizal colonization was highest (64%) at 150 mg kg−1 Si with SE, whereas AMF spore abundance decreased as Si increased. SE and 300 mg kg−1 Si raised the Si levels in the shoot, while root Si increased only at 300 mg kg−1 Si. Shoot Na increased at 300 mg kg−1 Si without SE, whereas K was highest at 150 mg kg−1 Si with SE. The soil pH, electrical conductivity, and Na increased at 300 mg kg−1 Si, while K and P decreased at this level without SE. These findings indicate that SE and Si co-application benefits early growth and may modulate mycorrhizal symbiosis, highlighting the importance of proper management to maximize plant and soil benefits.

Soils from Brazilian semiarid regions are highly vulnerable to desertification due to their geology, climate, human actions, and intensive land use that contribute to desertification. Therefore, areas under desertification have increased in the Brazilian semiarid region and it has negatively changed the soil bacterial and archaeal communities and their functionality. On the other hand, although restoration strategies are expensive and there are few soils restoration programs, some practices have been applied to restore these soils under desertification. For instance, conservationist practices and grazing exclusion have been strategically implemented, and they created a new altered soil condition for soil microbial communities, boosting soil microbial diversity. Here, we discuss the potential of these restoration strategies to recover the richness and diversity of soil bacterial and archaeal communities that were described through environmental DNA (eDNA) sequencing of soil samples. eDNA sequencing results show that areas where restoration strategies have been applied in regions under desertification in the Brazilian semiarid have increased species richness, diversity, and structure of the bacterial and archaeal community. In addition, network connectivity and functionality of the soil microorganisms have been improved over time. Altogether, we show that management strategies for soil restoration have positive effects on soil microbial communities and these effects can be monitored using the eDNA sequencing approach.

Minerals are the key factor determining human beings’ optimum growth and development. The deficiencies of minerals and vitamins hinder the human normal growth and development and economic status. In the 21st century, macro and micronutrient deficiencies are significant challenges to improving the nutritional value of foods at the socio-economic level. Bio-fortification is a simple strategy to improve the nutritional value of the human diet. Several bio-fortification strategies, including traditional breeding, transgenic, agronomic, and modernized agriculture practices, were employed to biofortify crops to meet nutritional needs. However, these strategies are also lacking sustainability due to the specific crop species and micronutrients, provision of long-term monitoring and assistance, long term high cost of special chemical fertilizers, losses of crop yield due to chemical fertilizers-induced alterations of plant metabolism, environmental and health impact originating from incorporation new minerals elements like Se and Cu. Therefore, microbial bio-fortification can promote human health and agriculture sustainability. This review highlights; the phyto-availability of micronutrients (Fe, Zn, Mg, Ca, Se, I, & Cu) for human diets; availability of micronutrients value in a stable in the edible part of plants; plant uptakes of micronutrients from the soil system; & strategies of crops fortification and its importance. At present, microbial bio-fortification should be emphasized by exploring the macro and micronutrients regulatory mechanisms through plant-microbe interaction with specific soil systems and climate change.

Soil fertility is key point to pastures systems and drives the microbial communities and their functionality. Therefore, an understanding of the interaction between soil fertility and microbial communities can increase our ability to manage pasturelands and maintain their soil functioning and productivity. This study probed the influence of soil fertility on microbial communities in tropical pastures in Brazil. Soil samples, gathered from the top 20 cm of twelve distinct areas with diverse fertility levels, were analyzed via 16S rRNA sequencing. The soils were subsequently classified into two categories, namely high fertility (HF) and low fertility (LF), using the K-Means clustering. The random forest analysis revealed that high fertility (HF) soils had more bacterial diversity, predominantly Proteobacteria, Nitrospira, Chloroflexi, and Bacteroidetes, while Acidobacteria increased in low fertility (LF) soils. High fertility (HF) soils exhibited more complex network interactions and an enrichment of nitrogen-cycling bacterial groups. Additionally, functional annotation based on 16S rRNA varied between clusters. Microbial groups in HF soil demonstrated enhanced functions such as nitrate reduction, aerobic ammonia oxidation, and aromatic compound degradation. In contrast, in the LF soil, the predominant processes were ureolysis, cellulolysis, methanol oxidation, and methanotrophy. Our findings expand our knowledge about how soil fertility drives bacterial communities in pastures.